Ok so I'm already past the lvl 25 GC quest, so I'm way past Ifrit, already finished the Ramuh quests for Twin Adders - I started in Ul'dah though.

I'm a 1.0 player, but no Legacy, I did get the chocobo whistle in 1.0, but I no longer have it. Anyways the item is not there on the quartermaster to purchase and I have well over 3k seals already too. Oddly enough my chocobo is listed as a companion in the character page but I have no ability to summon it, in town or outside through the chocobo command.

So I assume the ability isn't available under your "mount" tab? If so the Chocobo Insurance (I believe it is called) is listed under "material" at the quartermaster for 2k seals, if I am not mistaken. Also, if you don't have the quest, I dunno if it'll let you use the insurance tho. If nothing works, I would suggest talking to a GM. Who knows, maybe they'll fix your problems instead of throw out apologies for once, lol.

The Chocobo Issuance isn't there to purchase, that's the thing, I'm in the grand company already, the curious thing is I am a Private Second Class already, I think you're supposed to start out at Private Third class no? Well I got to Private Second Class in 1.0, and somehow I am 2nd class again in 1.0... I put in a GM ticket, waiting to hear back.

Oh wow this is hilarious! I actually completed the quest "My Little Chocobo" (Gridania) and it shows up in my quest log as complete, but lo and behold I have no chocobo whistle, not on the delivery moogle, my inventory, key items or retainer!!!